def test_classification_with_colon(self):
# since SMCOG id and description are stored in a string separated by :,
# ensure that descriptions containing : are properly handled
# test gene is AQF52_5530 from CP013129.1
translation = (
"MDTHQREEDPVAARRDRTHYLYLAVIGAVLLGIAVGFLAPGVAVELKPLGTGFVN"
"LIKMMISPIIFCTIVLGVGSVRKAAKVGAVGGLALGYFLVMSTVALAIGLLVGNL"
"LEPGSGLHLTKEIAEAGAKQAEGGGESTPDFLLGIIPTTFVSAFTEGEVLQTLLV"
"ALLAGFALQAMGAAGEPVLRGIGHIQRLVFRILGMIMWVAPVGAFGAIAAVVGAT"
"GAAALKSLAVIMIGFYLTCGLFVFVVLGAVLRLVAGINIWTLLRYLGREFLLILS"
"TSSSESALPRLIAKMEHLGVSKPVVGITVPTGYSFNLDGTAIYLTMASLFVAEAM"
"GDPLSIGEQISLLVFMIIASKGAAGVTGAGLATLAGGLQSHRPELVDGVGLIVGI"
"DRFMSEARALTNFAGNAVATVLVGTWTKEIDKARVTEVLAGNIPFDEKTLVDDHA"
"PVPVPDQRAEGGEEKARAGV")
cds = helpers.DummyCDS(0, len(translation))
cds.translation = translation
results = smcogs.classify("test", [cds], get_config())
assert results.best_hits[cds.get_name(
)].hit_id == "SMCOG1212:sodium:dicarboxylate symporter"
record = helpers.DummyRecord(seq=translation)
record.add_cds_feature(cds)
record.add_protocluster(helpers.DummyProtocluster(0, len(translation)))
# if we don't handle multiple semicolons right, this line will crash
results.add_to_record(record)
gene_functions = cds.gene_functions.get_by_tool("smcogs")
assert len(gene_functions) == 1
assert str(gene_functions[0]).startswith(
"transport (smcogs) SMCOG1212:sodium:dicarboxylate symporter"
" (Score: 416; E-value: 2.3e-126)")
def test_annotations(self):
results = smcogs.classify(self.record.id,
self.record.get_cds_features(), self.options)
results.add_to_record(self.record)
for cds in self.record.get_cds_features():
if cds.gene_functions.get_by_tool("rule-based-clusters"):
continue
assert cds.gene_function == results.function_mapping.get(
cds.get_name(), GeneFunction.OTHER)
def test_results_reconstruction(self):
results = smcogs.classify(self.record.id,
self.record.get_cds_features(), self.options)
assert results.tool == "smcogs"
assert results.best_hits[
"nisB"].hit_id == 'SMCOG1155:Lantibiotic dehydratase domain protein'
json = results.to_json()
assert json["best_hits"]["nisB"][
0] == 'SMCOG1155:Lantibiotic dehydratase domain protein'
reconstructed = core.FunctionResults.from_json(json, self.record)
assert reconstructed.tool == "smcogs"
assert reconstructed.best_hits[
"nisB"].hit_id == 'SMCOG1155:Lantibiotic dehydratase domain protein'
assert reconstructed.to_json() == json